Variant 10-63465484-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_032776.3(JMJD1C):c.168+11C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.773 in 1,589,650 control chromosomes in the GnomAD database, including 484,136 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.66 ( 36092 hom., cov: 34)

Exomes 𝑓: 0.78 ( 448044 hom. )

Consequence

JMJD1C
NM_032776.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.149

Variant links:

Genes affected

JMJD1C (HGNC:12313): (jumonji domain containing 1C) The protein encoded by this gene interacts with thyroid hormone receptors and contains a jumonji domain. It is a candidate histone demethylase and is thought to be a coactivator for key transcription factors. It plays a role in the DNA-damage response pathway by demethylating the mediator of DNA damage checkpoint 1 (MDC1) protein, and is required for the survival of acute myeloid leukemia. Mutations in this gene are associated with Rett syndrome and intellectual disability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]

JMJD1C links:

JMJD1C-AS1 (HGNC:):

JMJD1C-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BP6

Variant 10-63465484-G-C is Benign according to our data. Variant chr10-63465484-G-C is described in ClinVar as [Benign]. Clinvar id is 1170745.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
JMJD1C	NM_032776.3 linkuse as main transcript	c.168+11C>G		intron_variant		ENST00000399262.7	NP_116165.1	Q15652-1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
JMJD1C	ENST00000399262.7 linkuse as main transcript	c.168+11C>G	intron_variant		5	NM_032776.3	ENSP00000382204.2	Q15652-1
JMJD1C-AS1	ENST00000609436.1 linkuse as main transcript	n.256G>C	non_coding_transcript_exon_variant	1/1	6
JMJD1C	ENST00000633035.1 linkuse as main transcript	n.113+56254C>G	intron_variant		3

Frequencies

GnomAD3 genomes

AF:

0.661

AC:

100534

AN:

152112

Hom.:

36119

Cov.:

show subpopulations

Gnomad AFR

AF:

0.368

Gnomad AMI

AF:

0.809

Gnomad AMR

AF:

0.604

Gnomad ASJ

AF:

0.837

Gnomad EAS

AF:

0.696

Gnomad SAS

AF:

0.739

Gnomad FIN

AF:

0.825

Gnomad MID

AF:

0.671

Gnomad NFE

AF:

0.807

Gnomad OTH

AF:

0.659

GnomAD3 exomes

AF:

0.718

AC:

154868

AN:

215544

Hom.:

57823

AF XY:

0.736

AC XY:

87017

AN XY:

118290

show subpopulations

Gnomad AFR exome

AF:

0.355

Gnomad AMR exome

AF:

0.522

Gnomad ASJ exome

AF:

0.834

Gnomad EAS exome

AF:

0.687

Gnomad SAS exome

AF:

0.746

Gnomad FIN exome

AF:

0.825

Gnomad NFE exome

AF:

0.805

Gnomad OTH exome

AF:

0.752

GnomAD4 exome

AF:

0.784

AC:

1127601

AN:

1437420

Hom.:

448044

Cov.:

AF XY:

0.786

AC XY:

560743

AN XY:

713444

show subpopulations

Gnomad4 AFR exome

AF:

0.356

Gnomad4 AMR exome

AF:

0.532

Gnomad4 ASJ exome

AF:

0.830

Gnomad4 EAS exome

AF:

0.697

Gnomad4 SAS exome

AF:

0.752

Gnomad4 FIN exome

AF:

0.826

Gnomad4 NFE exome

AF:

0.812

Gnomad4 OTH exome

AF:

0.760

GnomAD4 genome

AF:

0.660

AC:

100502

AN:

152230

Hom.:

36092

Cov.:

AF XY:

0.663

AC XY:

49370

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.367

Gnomad4 AMR

AF:

0.603

Gnomad4 ASJ

AF:

0.837

Gnomad4 EAS

AF:

0.695

Gnomad4 SAS

AF:

0.739

Gnomad4 FIN

AF:

0.825

Gnomad4 NFE

AF:

0.807

Gnomad4 OTH

AF:

0.658

Alfa

AF:

0.720

Hom.:

5089

Bravo

AF:

0.627

Asia WGS

AF:

0.640

AC:

2225

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jan 06, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Early myoclonic encephalopathy

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 29, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

7.5

DANN

Benign

0.71

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.15

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over